|Abstract or Summary
- Automation of computational chemistry
- Automation of computational chemistry, while only an engineering feat, has the potential to accelerating computational research be removing all by the science. The work in this thesis mainly discusses fundamental understanding of complex chemical systems. What is not obvious are the numerous tasks necessary for this fundamental understanding. Under the surface automation and acceleration of many tedious and otherwise intractable tasks has made the research possible.Density functional theory computations of the Cu-catalyzed ring expansion of vinyloxiranes is mediated by a trace less dual Cu(I)-catalyst mechanism. Overall, the reaction involves a monomeric Cu(I)-catalyst, but a single key step, the Cu migration, requires two Cu(I)-catalysts for the transformation. This dual-Cu step is found to be a true double Cu(I) transition state rather than a single Cu(I) transition state in the presence of an adventitious, spectator Cu(I). Both Cu(I) catalysts are involved in the bond forming and breaking process. The single Cu(I) transition state is not a stationary point on the potential energy surface. Interestingly, the reductive elimination is rate-determining for the major diastereomeric product, while the Cu(I) migration step is rate-determining for the minor. Thus, while the reaction requires dual Cu(I) activation to proceed, kinetically, the presence of the dual-Cu(I) step is untraceable. The diastereospecificity of this reaction is controlled by the Cu migration step. Suprafacial migration is favored over antarafacial migration due to the distorted Cu π-allyl in the latter.The origins of differential catalytic reactivities of four Rh(I) catalysts and their derivatives in the (5 + 2) cycloaddition reaction were elucidated using density functional theory. Computed free energy spans are in excellent agreement with known experimental rates. For every catalyst, the substrate geometries in the transition state remained constant (<0.1 Å RMSD for atoms involved in bond-making and -breaking processes). Catalytic efficiency is shown to be a function of how well the catalyst accommodates the substrate transition state geometry and electronics. This shows that the induced fit model for explaining biological catalysis may be relevant to transition metal catalysis. This could serve as a general model for understanding the origins of efficiencies of catalytic reactions.The cross-coupling of allylzinc halides with aryl and vinyl electrophiles provides an effective means to access a wide range of prenylated arenes and “skipped dienes” in a completely linear-selective fashion, as demonstrated by a concise synthesis of the anti-HIV natural product siamenol. DFT calculations shed light on the origin of the excellent regioselectivity observed with the current Pd-based catalyst system.We computed band gaps of amorphous oxides within the In-Ga-Zn triad. These included ZnO, Ga₂O₃, In₂O₃, Ga₂ZnO₄, Ga₂Zn₈O₁₁, In₂ZnO₄, InGaZnO₄, and InGaO₃. Comparing the computed band gap to experimental measurements, the results were promising with a mean unsigned error of 0.28 eV and an unsigned standard deviation of 0.28 eV. Unfortunately drastic over prediction of the band gap for ZnO and InGaZnO₄ was observed.The ever acceleration of computational speed and efficiency is allowing for accurate computations of large and complex chemical systems. As these systems grow in size and complexity the number of data points grow exponentially. Traditionally computational chemists would do the tedious work of manually creating, submitting, examining and parsing all files and data points. With the use of both GPU acceleration and ηScripts, a library of tools, we have changed the intractable into the achievable and tedious into the pleasant.